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- PDB-2req: METHYLMALONYL-COA MUTASE, NON-PRODUCTIVE COA COMPLEX, IN OPEN CON... -

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Basic information

Entry
Database: PDB / ID: 2req
TitleMETHYLMALONYL-COA MUTASE, NON-PRODUCTIVE COA COMPLEX, IN OPEN CONFORMATION REPRESENTING SUBSTRATE-FREE STATE
Components(METHYLMALONYL-COA MUTASE) x 2
KeywordsISOMERASE / MUTASE / INTRAMOLECULAR TRANSFERASE
Function / homology
Function and homology information


lactate fermentation to propionate and acetate / methylmalonyl-CoA mutase / methylmalonyl-CoA mutase activity / cobalamin binding / metal ion binding
Similarity search - Function
Methylmalonyl-CoA mutase small subunit, N-terminal / Methylmalonyl-CoA mutase, beta chain / Methylmalonyl-CoA mutase signature. / Methylmalonyl-CoA mutase / Methylmalonyl-CoA mutase, alpha chain, catalytic / Methylmalonyl-CoA mutase, alpha/beta chain, catalytic / Methylmalonyl-CoA mutase / Methylmalonyl-CoA mutase, C-terminal / Cobalamin-binding domain / Cobalamin (vitamin B12)-dependent enzyme, catalytic ...Methylmalonyl-CoA mutase small subunit, N-terminal / Methylmalonyl-CoA mutase, beta chain / Methylmalonyl-CoA mutase signature. / Methylmalonyl-CoA mutase / Methylmalonyl-CoA mutase, alpha chain, catalytic / Methylmalonyl-CoA mutase, alpha/beta chain, catalytic / Methylmalonyl-CoA mutase / Methylmalonyl-CoA mutase, C-terminal / Cobalamin-binding domain / Cobalamin (vitamin B12)-dependent enzyme, catalytic / B12 binding domain / Cobalamin-binding domain superfamily / B12-binding domain profile. / Cobalamin (vitamin B12)-binding domain / TIM Barrel / Alpha-Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
COBALAMIN / COENZYME A / Methylmalonyl-CoA mutase small subunit / Methylmalonyl-CoA mutase large subunit
Similarity search - Component
Biological speciesPropionibacterium freudenreichii subsp. shermanii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsEvans, P.R. / Mancia, F.
Citation
Journal: Structure / Year: 1998
Title: Conformational changes on substrate binding to methylmalonyl CoA mutase and new insights into the free radical mechanism.
Authors: Mancia, F. / Evans, P.R.
#1: Journal: Structure / Year: 1996
Title: How Coenzyme B12 Radicals are Generated: The Crystal Structure of Methylmalonyl-Coenzyme a Mutase at 2 A Resolution
Authors: Mancia, F. / Keep, N.H. / Nakagawa, A. / Leadlay, P.F. / Mcsweeney, S. / Rasmussen, B. / Bosecke, P. / Diat, O. / Evans, P.R.
History
DepositionSep 22, 1997Processing site: BNL
Revision 1.0Jan 28, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 24, 2012Group: Non-polymer description
Revision 1.4Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: METHYLMALONYL-COA MUTASE
B: METHYLMALONYL-COA MUTASE
C: METHYLMALONYL-COA MUTASE
D: METHYLMALONYL-COA MUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)303,3328
Polymers299,1364
Non-polymers4,1964
Water11,458636
1
A: METHYLMALONYL-COA MUTASE
B: METHYLMALONYL-COA MUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,6664
Polymers149,5682
Non-polymers2,0982
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10650 Å2
ΔGint-65 kcal/mol
Surface area47720 Å2
MethodPISA
2
C: METHYLMALONYL-COA MUTASE
D: METHYLMALONYL-COA MUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,6664
Polymers149,5682
Non-polymers2,0982
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10660 Å2
ΔGint-63 kcal/mol
Surface area47680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.950, 162.060, 104.200
Angle α, β, γ (deg.)90.00, 108.75, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.320376, 0.104528, 0.941506), (-0.098588, -0.992175, 0.076605), (0.942146, -0.068279, 0.328175)
Vector: 34.739, 47.217, 49.393)
DetailsTHE CRYSTAL ASYMMETRIC UNIT CONSISTS OF TWO HETERODIMERIC MOLECULES, EACH WITH AN ACTIVE ALPHA CHAIN (CHAINS A AND C), AND AN INACTIVE BETA CHAIN (CHAINS B AND D). EACH ALPHA CHAIN CONTAINS A COBALAMIN, MODELLED AS A 5-COORDINATE CO(II) SPECIES, AND A COENZYME A MOLECULE APPROXIMATELY IN THE SUBSTRATE BINDING SITE, BUT WITH THE PANTOTHEINE SIDE CHAIN DISORDERED. THE WATERS ARE ASSOCIATED WITH PROTEIN CHAINS AS FOLLOWS: PROTEIN CHAINS WATERS A AND B X C AND D Y

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Components

#1: Protein METHYLMALONYL-COA MUTASE /


Mass: 80137.852 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: CHAINS A AND C INCLUDE COENZYME B12, AND COA. B12 IS PRESENT LARGELY AS REDUCED COB(II)ALAMIN, OR B12R. COA IS ONLY PARTLY ORDERED AND IS NOT BOUND CORRECTLY IN THE TRUE SUBSTRATE SITE
Source: (gene. exp.) Propionibacterium freudenreichii subsp. shermanii (bacteria)
Species: Propionibacterium freudenreichii / Strain: NCIB 9885
Description: THE 2 GENES MUTA (BETA CHAIN) AND MUTB (ALPHA CHAIN) ARE COEXPRESSED FROM THE SAME PLASMID
Gene: MUTA, MUTB / Plasmid: PMEX2 / Cellular location (production host): CYTOPLASM / Gene (production host): MUTA, MUTB / Production host: K38 PGP1-2 / References: UniProt: P11653, methylmalonyl-CoA mutase
#2: Protein METHYLMALONYL-COA MUTASE /


Mass: 69430.188 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: CHAINS A AND C INCLUDE COENZYME B12, AND COA. B12 IS PRESENT LARGELY AS REDUCED COB(II)ALAMIN, OR B12R. COA IS ONLY PARTLY ORDERED AND IS NOT BOUND CORRECTLY IN THE TRUE SUBSTRATE SITE
Source: (gene. exp.) Propionibacterium freudenreichii subsp. shermanii (bacteria)
Species: Propionibacterium freudenreichii / Strain: NCIB 9885
Description: THE 2 GENES MUTA (BETA CHAIN) AND MUTB (ALPHA CHAIN) ARE COEXPRESSED FROM THE SAME PLASMID
Gene: MUTA, MUTB / Plasmid: PMEX2 / Cellular location (production host): CYTOPLASM / Gene (production host): MUTA, MUTB / Production host: K38 PGP1-2 / References: UniProt: P11652, methylmalonyl-CoA mutase
#3: Chemical ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Chemical ChemComp-B12 / COBALAMIN / Vitamin B12


Mass: 1330.356 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C62H89CoN13O14P
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 636 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHIS STRUCTURE IS IN THE OPEN SUBSTRATE-FREE CONFORMATION, WITH THE SUBSTRATE ANALOGUE COA BOUND IN ...THIS STRUCTURE IS IN THE OPEN SUBSTRATE-FREE CONFORMATION, WITH THE SUBSTRATE ANALOGUE COA BOUND IN A NON-PRODUCTIVE MANNER.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56 % / Description: DATA COLLECTED AT ELETTRA, TRIESTE, ITALY
Crystal growMethod: vapor diffusion / pH: 7.5
Details: PROTEIN SOLUTION: 20 MG/ML PROTEIN, 1MM ADENOSYLCOBALAMIN, 2MM COA, 1MM DTT, TRIS -HCL PH 7.5. RESERVOIR SOLUTION: 17.5% (W/V) PEG4000, 20% GLYCEROL (V/V), 100MM TRIS-HCL PH 7.5. EQUAL ...Details: PROTEIN SOLUTION: 20 MG/ML PROTEIN, 1MM ADENOSYLCOBALAMIN, 2MM COA, 1MM DTT, TRIS -HCL PH 7.5. RESERVOIR SOLUTION: 17.5% (W/V) PEG4000, 20% GLYCEROL (V/V), 100MM TRIS-HCL PH 7.5. EQUAL VOLUMES OF PROTEIN SOLUTION WERE MIXED AND EQUILIBRATED BY VAPOR DIFFUSION., vapor diffusion
Crystal grow
*PLUS
Temperature: 23 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
21 mMcoenzyme B121drop
32 mMCoA1drop
41 mMdithiothreitol1drop
617.5 %(w/v)PEG40001reservoir
720 %(v/v)glycerol1reservoir
8100 mMTris-HCl1reservoir
5Tris-HCl1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.24
DetectorType: MAR scanner 180 mm plate / Detector: IMAGE PLATE / Date: Jul 1, 1995 / Details: TOROIDAL MIRROR, SI MONOCHROMATOR
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.24 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 113512 / % possible obs: 99.8 % / Observed criterion σ(I): 3.5 / Redundancy: 4.8 % / Biso Wilson estimate: 55 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 6
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.338 / Mean I/σ(I) obs: 2.1 / % possible all: 99.7
Reflection shell
*PLUS
Highest resolution: 2.5 Å / % possible obs: 99.7 %

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Processing

Software
NameVersionClassification
AMoREphasing
REFMACrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1REQ

1req


Resolution: 2.5→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.325 4538 5 %RANDOM
Rwork0.259 ---
obs-113303 99.6 %-
Displacement parametersBiso mean: 47 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20360 0 244 636 21240
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0120.02
X-RAY DIFFRACTIONp_angle_d0.0410.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0460.05
X-RAY DIFFRACTIONp_hb_or_metal_coord0.1
X-RAY DIFFRACTIONp_mcbond_it2.4243
X-RAY DIFFRACTIONp_mcangle_it3.745
X-RAY DIFFRACTIONp_scbond_it3.7134
X-RAY DIFFRACTIONp_scangle_it5.1026
X-RAY DIFFRACTIONp_plane_restr0.030.03
X-RAY DIFFRACTIONp_chiral_restr0.1410.15
X-RAY DIFFRACTIONp_singtor_nbd0.1290.15
X-RAY DIFFRACTIONp_multtor_nbd0.170.15
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1280.15
X-RAY DIFFRACTIONp_planar_tor5.97
X-RAY DIFFRACTIONp_staggered_tor19.815
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor34.420
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Num. reflection all: 113303 / Rfactor all: 0.259
Solvent computation
*PLUS
Displacement parameters
*PLUS

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